A unique genetic signature for cancer-associated fibroblasts in Melanoma metastases

Cancer-associated fibroblasts (CAFs) represent a central population of the tumor microenvironment (TME). Recently, single-cell RNA sequencing (scRNA-seq) analyes of primary tumors of different cancer entities yielded different classifications of CAF subsets underscoring heterogeneity of CAFs within the TME. Here, we analyzed the transcriptional signatures of approximately 8,400 CAFs and normal fibroblasts by scRNA-seq and compared genetic profiles of CAFs from murine melanoma primary tumors to CAFs from corresponding melanoma lung metastases. This revealed distinct subsets for primary tumor and metastasis specific CAF populations, respectively. Combined with spatial characterization of metastasis CAFs at the RNA and protein level, scRNA-analyses indicate a tumor-dependent crosstalk between neutrophils and CAFs, mediated via SAA3 and IL1b related signaling pathways, which can be recapitulated in vitro. Importantly, analyzing tissue sections of human patient samples this link was found to be present in human melanoma metastasis. Taken together, our data highlights unique characteristics of metastasis CAFs with potential therapeutic impact for melanoma metastasis. Melanoma cells and cells from the tumor microenvironment were isolated from tumor and metastasis bearing mT/mG mice and FACS sorted based on tdTomato expression and analyzed by scRNA sequencing.